rs1952224

chr2-214907688-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_110292.1(SNHG31):n.322-40137G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 152,074 control chromosomes in the GnomAD database, including 11,567 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.39 (11567 hom., cov: 33)
• Consequence: SNHG31 NR_110292.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

Genes affected

SNHG31 (HGNC:54196): (small nucleolar RNA host gene 31)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNHG31	NR_110292.1	n.322-40137G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNHG31	ENST00000670391.1	n.438-54122G>A		intron_variant, non_coding_transcript_variant
SNHG31	ENST00000607412.1	n.322-40137G>A		intron_variant, non_coding_transcript_variant		2
SNHG31	ENST00000655899.1	n.370-52705G>A		intron_variant, non_coding_transcript_variant
SNHG31	ENST00000664818.1	n.334-54122G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59245 AN: 151958 Hom.: 11557 Cov.: 33

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.394

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.390 AC: 59278 AN: 152074 Hom.: 11567 Cov.: 33 AF XY: 0.391 AC XY: 29057 AN XY: 74332

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.393

Alfa AF: 0.394 Hom.: 5986

Bravo AF: 0.384

Asia WGS AF: 0.372 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
Cadd	Benign	14
Dann	Benign	0.65

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1952224; hg19: chr2-215772412;